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Basic information

Entry
Database: PDB / ID: 6lsa
TitleComplex structure of bovine herpesvirus 1 glycoprotein D and bovine nectin-1 IgV
Components
  • Envelope glycoprotein D
  • Nectin cell adhesion molecule 1
KeywordsVIRAL PROTEIN / complex structure
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / Adherens junctions interactions / protein localization to cell junction / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / adherens junction / viral envelope / membrane
Similarity search - Function
Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / : / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain ...Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / : / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Distorted Sandwich / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nectin cell adhesion molecule 1 / Glycoprotein D
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Bovine alphaherpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsYue, D. / Chen, Z.J. / Yang, F.L. / Ye, F. / Lin, S. / Cheng, Y.W. / Wang, J.C. / Chen, Z.M. / Lin, X. / Yang, J. ...Yue, D. / Chen, Z.J. / Yang, F.L. / Ye, F. / Lin, S. / Cheng, Y.W. / Wang, J.C. / Chen, Z.M. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z.L. / You, Y. / Sun, H.L. / Wen, A. / Wang, L.L. / Zheng, Y. / Cao, Y. / Li, Y.H. / Lu, G.W.
CitationJournal: Sci Adv / Year: 2020
Title: Crystal structure of bovine herpesvirus 1 glycoprotein D bound to nectin-1 reveals the basis for its low-affinity binding to the receptor.
Authors: Yue, D. / Chen, Z. / Yang, F. / Ye, F. / Lin, S. / He, B. / Cheng, Y. / Wang, J. / Chen, Z. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z. / You, Y. / Sun, H. / Wen, A. / Wang, L. / Zheng, Y. / ...Authors: Yue, D. / Chen, Z. / Yang, F. / Ye, F. / Lin, S. / He, B. / Cheng, Y. / Wang, J. / Chen, Z. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z. / You, Y. / Sun, H. / Wen, A. / Wang, L. / Zheng, Y. / Cao, Y. / Li, Y. / Lu, G.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nectin cell adhesion molecule 1
F: Envelope glycoprotein D
B: Nectin cell adhesion molecule 1
C: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8127
Polymers93,9454
Non-polymers8673
Water3,585199
1
A: Nectin cell adhesion molecule 1
F: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1943
Polymers46,9722
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nectin cell adhesion molecule 1
C: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6184
Polymers46,9722
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.871, 64.234, 102.931
Angle α, β, γ (deg.)90.000, 91.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-1159-

HOH

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Components

#1: Protein Nectin cell adhesion molecule 1


Mass: 12100.761 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: NECTIN1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F1MQJ3
#2: Protein Envelope glycoprotein D / Glycoprotein D


Mass: 34871.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine alphaherpesvirus 1
Gene: US6, gD, AAADCAAH_00066, BLEONNCJ_00068, BLPDLEPH_00067, DCJDKEDG_00068, DILPLKIK_00066, DJCKHMNK_00067, HMKIDIGP_00066, LALCDEHK_00068, NBBNDGNH_00066, NCKHNGOI_00066, NFOBEAPH_00067, OCMKPLLD_ ...Gene: US6, gD, AAADCAAH_00066, BLEONNCJ_00068, BLPDLEPH_00067, DCJDKEDG_00068, DILPLKIK_00066, DJCKHMNK_00067, HMKIDIGP_00066, LALCDEHK_00068, NBBNDGNH_00066, NCKHNGOI_00066, NFOBEAPH_00067, OCMKPLLD_00067, OHMFJBFK_00067
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q76PF1
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Sodium HEPES, 15% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 58498 / % possible obs: 98.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.9
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.783 / Num. unique obs: 5751

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16-3549refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X5W

5x5w


Resolution: 2.204→45.196 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.38
RfactorNum. reflection% reflection
Rfree0.2362 2905 4.97 %
Rwork0.1995 --
obs0.2013 58439 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.66 Å2 / Biso mean: 61.8638 Å2 / Biso min: 27.92 Å2
Refinement stepCycle: final / Resolution: 2.204→45.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5680 0 56 199 5935
Biso mean--84.92 56.42 -
Num. residues----706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115932
X-RAY DIFFRACTIONf_angle_d1.3378098
X-RAY DIFFRACTIONf_chiral_restr0.067844
X-RAY DIFFRACTIONf_plane_restr0.0071045
X-RAY DIFFRACTIONf_dihedral_angle_d20.9853498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2041-2.24020.3051310.3143235188
2.2402-2.27880.29731490.2865258097
2.2788-2.32030.32991370.2826263698
2.3203-2.36490.24971200.2501268399
2.3649-2.41320.30731260.2579264699
2.4132-2.46560.3081360.2609267298
2.4656-2.5230.30021410.2456247392
2.523-2.58610.29241500.2435267599
2.5861-2.6560.24581380.21912685100
2.656-2.73410.27021280.2185265299
2.7341-2.82240.24841470.2302269799
2.8224-2.92320.27561460.2291267199
2.9232-3.04020.26611430.22642695100
3.0402-3.17860.23581230.2213269099
3.1786-3.34610.26141620.2111246193
3.3461-3.55570.26121300.20852764100
3.5557-3.83010.22471110.18962726100
3.8301-4.21520.23641380.17612720100
4.2152-4.82460.18831400.1482260595
4.8246-6.07620.19151370.16612757100
6.0762-45.1960.20561720.1872269596
Refinement TLS params.Method: refined / Origin x: -41.252 Å / Origin y: -31.543 Å / Origin z: 30.269 Å
111213212223313233
T0.3597 Å20.0356 Å2-0.0048 Å2-0.323 Å20.008 Å2--0.3152 Å2
L1.0206 °2-0.1371 °2-0.0662 °2-0.2 °20.0862 °2--0.3809 °2
S0.0617 Å °0.2382 Å °0.0209 Å °-0.0121 Å °-0.0694 Å °0.0291 Å °0.0124 Å °0.0164 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 109
2X-RAY DIFFRACTION1allA201 - 212
3X-RAY DIFFRACTION1allC6 - 249
4X-RAY DIFFRACTION1allC1001 - 1003
5X-RAY DIFFRACTION1allC1101 - 1179
6X-RAY DIFFRACTION1allB1 - 109
7X-RAY DIFFRACTION1allB201 - 209
8X-RAY DIFFRACTION1allF1101 - 1198
9X-RAY DIFFRACTION1allF6 - 249
10X-RAY DIFFRACTION1allF1001

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